EP2283148A2 - Cytological methods for detecting cancer - Google Patents
Cytological methods for detecting cancerInfo
- Publication number
- EP2283148A2 EP2283148A2 EP09734182A EP09734182A EP2283148A2 EP 2283148 A2 EP2283148 A2 EP 2283148A2 EP 09734182 A EP09734182 A EP 09734182A EP 09734182 A EP09734182 A EP 09734182A EP 2283148 A2 EP2283148 A2 EP 2283148A2
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- EP
- European Patent Office
- Prior art keywords
- cancer
- expression
- level
- cells
- normal
- Prior art date
- Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6809—Methods for determination or identification of nucleic acids involving differential detection
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
- C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
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- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
- G16B25/10—Gene or protein expression profiling; Expression-ratio estimation or normalisation
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/112—Disease subtyping, staging or classification
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/118—Prognosis of disease development
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/154—Methylation markers
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- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
Definitions
- the present invention relates to methods for diagnostics, detection or research analysis of cancer.
- the present invention is in the field of analysis of the levels of gene expression in normal or noncancerous cells because of their proximity to cancer cells.
- the present invention further provides for analysis of the altered gene expression levels in normal or noncancerous cells as an indicator of disease presence, positioning, prognosis, staging and grading.
- Prostate cancer is usually diagnosed by pathologists examining needle core biopsies collected from patients by urologists. There is a deficiency in the current art whereby biopsy sampling is insufficient to detect all prostate cancer tumors. In current practice, a urologist may collect six to twelve and possibly more needle core biopsies from a single patient in the hope of having at least one of the biopsy cores sample a patient's tumor.
- the current invention is a means to increase the sensitivity of needle core biopsies to detect the presence of prostate cancer.
- the current invention may have applications supporting the diagnosis of other cancers.
- This disclosure will also discuss possible application of the current invention to the detection of cancers of the bladder and breast. This is not intended to be an exhaustive list of the possible applications of the current invention. There are certainly other applications of the current invention for the detection of cancer.
- the present invention relates to methods for diagnostics, detection or research analysis of cancer.
- the present invention is in the field of analysis of the levels of gene expression in normal or noncancerous cells because of their proximity to cancer cells.
- the present invention further provides for analysis of the altered gene expression levels in normal or noncancerous cells as an indicator of disease presence, positioning, prognosis, staging and grading.
- a method for diagnosing the presence or absence of cancer in a patient.
- the method comprises the steps of: detecting the level of gene expression in anatomically normal or noncancerous cells in a cytology specimen consisting of cells that had previously resided in the proximity of cancer; wherein differential expression of the genes is indicative of cancer.
- a method for diagnosing the presence or absence of cancer in a patient.
- the method comprises the steps of: detecting the level of gene expression in anatomically normal or noncancerous cells in a cytology specimen consisting of cells that had previously resided in the proximity of cancer;; wherein increased expression of the genes that are up- regulated is indicative of cancer.
- a method for diagnosing the presence or absence of cancer in a patient.
- the method comprises the steps of: detecting the level of gene expression in anatomically normal or noncancerous cells in a cytology specimen consisting of cells that had previously resided in the proximity of cancer;; wherein increased expression of the genes that are down- regulated is indicative of cancer.
- Another aspect of the invention is a method of detecting the progression of cancer in a patient.
- the method comprises the steps of: detecting the level of gene expression in anatomically normal or noncancerous cells in a cytology specimen consisting of cells that had previously resided in the proximity of cancer;; wherein the differential expression of the genes is indicative of the cancer progression.
- Another aspect of the invention is a method of detecting the progression of cancer in a patient. The method comprises the steps of: detecting the level of gene expression in anatomically normal or noncancerous cells in a cytology specimen consisting of cells that had previously resided in the proximity of cancer;; wherein increased expression of the genes that are down-regulated is indicative of cancer progression.
- Another aspect of the invention is a method of detecting the progression of cancer in a patient.
- the method comprises the steps of: detecting the level of gene expression in anatomically normal or noncancerous cells in a cytology specimen consisting of cells that had previously resided in the proximity of cancer;; wherein increased expression of the genes that are up-regulated is indicative of cancer progression.
- the invention also includes methods of differentiating metastatic cancer from nonmetastatic cancer in a patient comprising the step of detecting the level of expression in anatomically normal or noncancerous cells in a cytology specimen consisting of cells that had previously resided in the proximity of cancer; wherein altered patterns of gene expression is indicative of metastatic cancer rather than nonmetastatic cancer.
- a method for diagnosing the presence or absence of cancer in a patient can be used to detect, for example, prostate cancer, bladder cancer, liver cancer, lung cancer, and breast cancer, just to name a few examples.
- the tumor is a gastrointestinal tumor, for example a tumor of the esophagus, the stomach, the pancreas, the bile tree, the liver, the small intestine, the colon or the rectum.
- the tumor is for example cancer of the esophagus, gastric cancer, cancer of the gallbladder, the pancreas, the liver, the small intestine, the colon or the rectum.
- the tumors according to the present invention may comprise tumors, which show detectable lymph-node involvement (node positive tumors) as well as tumors, without detectable spread to lymph nodes (node negative tumors).
- the gastrointestinal tumors are tumors without detectable spread to lymph nodes.
- Poor clinical outcome can be measured, for example, in terms of shortened survival or increased risk of cancer recurrence, e.g. following surgical removal of the cancer.
- the invention concerns a method of predicting the likelihood of the recurrence of cancer, following treatment, in a cancer patient, comprising determining the expression level of certain genes, or its expression product, in a cancer tissue obtained from the patient, normalized against a control gene or genes, and compared to the amount found in a reference cancer tissue set, wherein an expression level indicates decreased risk of recurrence following treatment.
- All types of cancer are included, such as, for example, breast cancer, colon cancer, lung cancer, prostate cancer, hepatocellular cancer, gastric cancer, pancreatic cancer, cervical cancer, ovarian cancer, liver cancer, bladder cancer, cancer of the urinary tract, thyroid cancer, renal cancer, carcinoma, melanoma, and brain cancer.
- the foregoing methods are particularly suitable for prognosis/classification of breast cancer.
- the expression level is determined using RNA obtained from a formalin-fixed, paraffin-embedded tissue sample. While all techniques of gene expression profiling, as well as proteomics techniques, are suitable for use in performing the foregoing aspects of the invention, the gene expression levels are often determined by reverse transcription polymerase chain reaction (RT-PCR).
- RT-PCR reverse transcription polymerase chain reaction
- the expression data can be further subjected to multivariate analysis, for example using the Cox Proportional Hazards model.
- the invention further includes computer systems comprising a database containing information identifying the expression level in an identified tissue of a set of genes; and a user interface to view the information.
- the database may further include sequence information for the genes, information identifying the expression level for the set of genes in normal tissue and malignant tissue (metastatic and nonmetastatic) and may contain links to external databases such as GenBank.
- the invention includes methods of using the databases, such as methods of using the disclosed computer systems to present information identifying the expression level in a tissue or cell, comprising the step of comparing the expression level in the tissue or cell to the level of expression of the gene in the database.
- microarray refers to an ordered arrangement of hybridizable array elements, preferably polynucleotide probes, on a substrate.
- polynucleotide when used in singular or plural, generally refers to any polyribonucleotide or polydeoxribonucleotide, which may be unmodified RNA or DNA or modified RNA or DNA.
- polynucleotides as defined herein include, without limitation, single- and double- stranded DNA, DNA including single- and double- stranded regions, single- and double- stranded RNA, and RNA including single- and double- stranded regions, hybrid molecules comprising DNA and RNA that may be single- stranded or, more typically, double-stranded or include single- and double- stranded regions.
- polynucleotide refers to triple-stranded regions comprising RNA or DNA or both RNA and DNA.
- the strands in such regions may be from the same molecule or from different molecules.
- the regions may include all of one or more of the molecules, but more typically involve only a region of some of the molecules.
- One of the molecules of a triple-helical region often is an oligonucleotide.
- polynucleotide specifically includes DNAs and RNAs that contain one or more modified bases. Thus, DNAs or RNAs with backbones modified for stability or for other reasons are "polynucleotides" as that term is intended herein.
- DNAs or RNAs comprising unusual bases, such as inosine, or modified bases, such as tritiated bases are included within the term “polynucleotides” as defined herein.
- polynucleotide embraces all chemically, enzymatically and/or metabolically modified forms of unmodified polynucleotides, as well as the chemical forms of DNA and RNA characteristic of viruses and cells, including simple and complex cells.
- oligonucleotide refers to a relatively short polynucleotide, including, without limitation, single-stranded deoxyribonucleotides, single- or double- stranded ribonucleotides, RNA:DNA hybrids and double-stranded DNAs. Oligonucleotides, such as single- stranded DNA probe oligonucleotides, are often synthesized by chemical methods, for example using automated oligonucleotide synthesizers that are commercially available. However, oligonucleotides can be made by a variety of other methods, including in vitro recombinant DNA- mediated techniques and by expression of DNAs in cells and organisms.
- RNA expression refers to the process of converting genetic information encoded in a gene into RNA (e.g., mRNA, rRNA, tRNA, or snRNA) through "transcription" of the gene (i.e., via the enzymatic action of an RNA polymerase), and for protein encoding genes, into protein through “translation” of mRNA.
- Gene expression can be regulated at many stages in the process.
- Up-regulation” or “activation” refers to regulation that increases the production of gene expression products (i.e., RNA or protein), while “down- regulation” or “repression” refers to regulation that decrease production.
- Molecules e.g., transcription factors
- activators e.g., transcription factors
- differentially expressed gene refers to a gene whose expression is activated to a higher or lower level in a subject suffering from a disease, specifically cancer, such as breast cancer, relative to its expression in a normal or control subject.
- the terms also include genes whose expression is activated to a higher or lower level at different stages of the same disease. It is also understood that a differentially expressed gene may be either activated or inhibited at the nucleic acid level or protein level, or may be subject to alternative splicing to result in a different polypeptide product.
- Differential gene expression may include a comparison of expression between two or more genes, or a comparison of the ratios of the expression between two or more genes, or even a comparison of two differently processed products of the same gene, which differ between normal subjects and subjects suffering from a disease, specifically cancer, or between various stages of the same disease.
- Differential expression includes both quantitative, as well as qualitative, differences in the temporal or cellular expression pattern in a gene or its expression products among, for example, normal and diseased cells, or among cells which have undergone different disease events or disease stages.
- differential gene expression is considered to be present when there is a measurable and statistically significant change in the abundance of a gene's mRNA and/or encoded protein product relative to another gene's or genes' mRNA(s) and /or encoded protein(s) abundance.
- a gene is differentially expressed if the abundance of its mRNA and/or its encoded protein changes relative to the abundance of one other gene's mRNA and/or protein.
- a gene is differentially expressed if its mRNA and/or encoded protein abundance changes relative to the abundances of the mRNAs and/or encoded proteins derived from two or more and possible all other genes.
- the phrase "gene amplification” refers to a process by which multiple copies of a gene or gene fragment are formed in a particular cell or cell line.
- the duplicated region (a stretch of amplified DNA) is often referred to as "amplicon.”
- amplicon a stretch of amplified DNA
- the amount of the messenger RNA (mRNA) produced i.e., the level of gene expression, may also increase in the proportion of the number of copies made of the particular gene expressed.
- the term "prognosis” is used herein to refer to the prediction of the likelihood of cancer-attributable death or progression, including recurrence, metastatic spread, and drug resistance, of a neoplastic disease, such as breast cancer.
- prediction is used herein to refer to the likelihood that a patient will respond either favorably or unfavorably to a drug or set of drugs, and also the extent of those responses.
- the predictive methods of the present invention can be used clinically to make treatment decisions by choosing the most appropriate treatment modalities for any particular patient.
- the predictive methods of the present invention are valuable tools in predicting if a patient is likely to respond favorably to a treatment regimen, such as surgical intervention, chemotherapy with a given drug or drug combination, and/or radiation therapy.
- Patient response can be assessed using any endpoint indicating a benefit to the patient, including, without limitation, (1) inhibition, to some extent, of tumor growth, including slowing down and complete growth arrest; (2) reduction in the number of tumor cells; (3) reduction in tumor size; (4) inhibition (i.e., reduction, slowing down or complete stopping) of tumor cell infiltration into adjacent peripheral organs and/or tissues; (5) inhibition (i.e.
- treatment refers to both therapeutic treatment and prophylactic or preventative measures, wherein the object is to prevent or slow down (lessen) the targeted pathologic condition or disorder.
- Those in need of treatment include those already with the disorder as well as those prone to have the disorder or those in whom the disorder is to be prevented.
- a therapeutic agent may directly decrease the pathology of tumor cells, or render the tumor cells more susceptible to treatment by other therapeutic agents, e.g., radiation and/or chemotherapy.
- tumor refers to all neoplastic cell growth and proliferation, whether malignant or benign, and all pre-cancerous and cancerous cells and tissues.
- cancer and “cancerous” refer to or describe the physiological condition in mammals that is typically characterized by unregulated cell growth. Examples of cancer include but are not limited to, breast cancer, colon cancer, lung cancer, prostate cancer, hepatocellular cancer, gastric cancer, pancreatic cancer, cervical cancer, ovarian cancer, liver cancer, bladder cancer, cancer of the urinary tract, thyroid cancer, renal cancer, carcinoma, melanoma, and brain cancer.
- the "pathology" of cancer includes all phenomena that compromise the well- being of the patient. This includes, without limitation, abnormal or uncontrollable cell growth, metastasis, interference with the normal functioning of neighboring cells, release of cytokines or other secretory products at abnormal levels, suppression or aggravation of inflammatory or immunological response, neoplasia, premalignancy, malignancy, invasion of surrounding or distant tissues or organs, such as lymph nodes, etc.
- a cytology specimen is a sampling of cells from an organ, tissue, bodily fluid or other region of the body.
- a key feature of a cytology specimen is that the cells in such a cytology specimen are disaggregated and occur singly or in small clusters. Information concerning the anatomical context of exactly where in the organ, tissue, bodily fluid or region of the body from which a cell in a cytology specimen was obtained cannot be directly observed.
- cytology specimens are collected as suspensions of cells and/or small clusters of cells in a fluid medium of some kind.
- the cells and cell clusters in a cytology specimen can be collected or concentrated by centrifugation or filtration.
- a cytology specimen can mean the cellular suspensions and/or their simple derivatives created by centrifugation or filtration.
- a "cytology sample” encompasses any sample obtained from a living system or subject.
- the definition encompasses blood, serum, tissue, and other samples of biological origin that can be collected from a living system, subject or individual.
- biological samples are obtained through sampling by minimally invasive or non-invasive approaches (e.g., urine collection, stool collection, blood drawing, needle aspiration, and other procedures involving minimal risk, discomfort or effort).
- Cytology samples are often liquid (sometimes referred to as a "biological fluid").
- Liquid cytology samples include, but are not limited to, urine, blood, interstitial fluid, edema fluid, saliva, lacrimal fluid, inflammatory exudates, synovial fluid, abscess, empyema or other infected fluid, cerebrospinal fluid, sweat, pulmonary secretions (sputum), seminal fluid, feces, bile, intestinal secretions, and others.
- Cytology samples include samples that have been manipulated in any way after their procurement, such as by treatment with reagents, various fixatives, solubilization, or enrichment for certain components, such as proteins or polynucleotides.
- the term "cytology sample” also encompasses a clinical sample such as serum, plasma, other biological fluid, or tissue samples, and also includes cells in culture, cell supernatants and cell lysates.
- normal or noncancerous means anatomically normal or noncancerous appearing when viewed with the aid of a microscope.
- Cells that appear normal or noncancerous may have altered patterns of gene expression and/or altered physiologies that may be indicative of or associated with a pathological state.
- the present invention relates to methods for diagnostics, detection or research analysis of cancer.
- the present invention is in the field of analysis of the levels of gene expression in normal or noncancerous cells because of their proximity to cancer cells.
- the present invention further provides for analysis of the altered gene expression levels in normal or noncancerous cells as an indicator of disease presence, positioning, prognosis, staging and grading.
- a method for diagnosing the presence or absence of cancer in a patient.
- the method comprises the steps of: detecting the level of gene expression in anatomically normal or noncancerous cells in a cytology specimen consisting of cells that had previously resided in the proximity of cancer; wherein differential expression of the genes is indicative of cancer.
- a method for diagnosing the presence or absence of cancer in a patient.
- the method comprises the steps of: detecting the level of gene expression in anatomically normal or noncancerous cells in a cytology specimen consisting of cells that had previously resided in the proximity of cancer;; wherein increased expression of the genes that are up- regulated is indicative of cancer.
- a method for diagnosing the presence or absence of cancer in a patient.
- the method comprises the steps of: detecting the level of gene expression in anatomically normal or noncancerous cells in a cytology specimen consisting of cells that had previously resided in the proximity of cancer;; wherein increased expression of the genes that are down- regulated is indicative of cancer.
- Another aspect of the invention is a method of detecting the progression of cancer in a patient.
- the method comprises the steps of: detecting the level of gene expression in anatomically normal or noncancerous cells in a cytology specimen consisting of cells that had previously resided in the proximity of cancer;; wherein the differential expression of the genes is indicative of the cancer progression.
- Another aspect of the invention is a method of detecting the progression of cancer in a patient.
- the method comprises the steps of: detecting the level of gene expression in anatomically normal or noncancerous cells in a cytology specimen consisting of cells that had previously resided in the proximity of cancer;; wherein increased expression of the genes that are down-regulated is indicative of cancer progression.
- Another aspect of the invention is a method of detecting the progression of cancer in a patient.
- the method comprises the steps of: detecting the level of gene expression in anatomically normal or noncancerous cells in a cytology specimen consisting of cells that had previously resided in the proximity of cancer;; wherein increased expression of the genes that are up-regulated is indicative of cancer progression.
- the invention also includes methods of differentiating metastatic cancer from nonmetastatic cancer in a patient comprising the step of detecting the level of expression in anatomically normal or noncancerous cells in a cytology specimen consisting of cells that had previously resided in the proximity of cancer; wherein altered patterns of gene expression is indicative of metastatic cancer rather than nonmetastatic cancer.
- a method for diagnosing the presence or absence of cancer in a patient can be used to detect, for example, prostate cancer, bladder cancer, liver cancer, lung cancer, and breast cancer, just to name a few examples.
- the tumor is a gastrointestinal tumor, for example a tumor of the esophagus, the stomach, the pancreas, the bile tree, the liver, the small intestine, the colon or the rectum.
- the tumor is for example cancer of the esophagus, gastric cancer, cancer of the gallbladder, the pancreas, the liver, the small intestine, the colon or the rectum.
- the tumors according to the present invention may comprise tumors, which show detectable lymph-node involvement (node positive tumors) as well as tumors, without detectable spread to lymphnodes (node negative tumors).
- the gastrointestinal tumors are tumors without detectable spread to lymph nodes.
- Poor clinical outcome can be measured, for example, in terms of shortened survival or increased risk of cancer recurrence, e.g. following surgical removal of the cancer.
- the invention concerns a method of predicting the likelihood of the recurrence of cancer, following treatment, in a cancer patient, comprising determining the expression level of certain genes, or its expression product, in a cancer tissue obtained from the patient, normalized against a control gene or genes, and compared to the amount found in a reference cancer tissue set, wherein an expression level indicates decreased risk of recurrence following treatment.
- the expression level is determined using RNA obtained from a formalin-fixed, paraffin-embedded tissue sample. While all techniques of gene expression profiling, as well as proteomics techniques, are suitable for use in performing the foregoing aspects of the invention, the gene expression levels are often determined by reverse transcription polymerase chain reaction (RT-PCR).
- RT-PCR reverse transcription polymerase chain reaction
- the expression data can be further subjected to multivariate analysis, for example using the Cox Proportional Hazards model.
- the invention further includes computer systems comprising a database containing information identifying the expression level in an identified tissue of a set of genes; and a user interface to view the information.
- the database may further include sequence information for the genes, information identifying the expression level for the set of genes in normal tissue and malignant tissue (metastatic and nonmetastatic) and may contain links to external databases such as GenBank.
- the invention includes methods of using the databases, such as methods of using the disclosed computer systems to present information identifying the expression level in a tissue or cell, comprising the step of comparing the expression level in the tissue or cell to the level of expression of the gene in the database.
- the invention is used to detect cancer by examining cytology specimens of normal (non-cancerous) cells for the differential expression of genes occurring as a consequence of these normal cells having been in the proximity of cancer cells.
- the invention is also used to detect cancer by examining cytology specimens of normal (non-cancerous) cells for the increased expression of the genes that are up-regulated as a consequence of these normal cells being in the proximity of cancer cells.
- the invention is also to detect cancer by examining cytology specimens of normal (non-cancerous) cells for the increased expression of the genes that are down-regulated as a consequence of these normal cells being in the proximity of cancer cells.
- the reference gene expression profile is contained within a database.
- the comparing of profiles is carried out using a computer algorithm.
- the method further comprises isolating the cell of the sample from the patient.
- the method further comprises preparing the patient's gene expression profile.
- the method further comprises: (c) providing a gene expression profile of a cell from the patient after the patient has undergone a treatment regimen for a disease state; and (d) comparing the post-treatment patient gene expression profile to the reference gene expression profile, to monitor the patient's response to the treatment regimen.
- the method provides for diagnosing a cancer disease state in a patient, the method comprising: (a) providing a gene expression profile of a patient's isolated cells wherein the isolated cells simultaneously express a plurality of genes at the protein level that are markers for specific for a disease; and (b) comparing the patient's gene expression profile to a reference gene expression profile obtained from a normal cell, wherein the reference gene expression profile comprises an expression value of a target gene, wherein differential expression of the target gene is indicative of a disease state, and wherein the disease state is a proliferative or hyperproliferative disorder.
- the proliferative or hyperproliferative disorder is cancer.
- the reference gene expression profile comprises an expression value of a target gene selected from the group consisting of human mRNA for one or more biomarker.
- an alteration in the level of the one or more biomarkers as compared to control indicates colorectal cancer or pre-malignant colorectal cancer state.
- the one or more biomarkers are chosen from a nucleic acid, a DNA, a RNA, and a protein.
- the alteration in the level of one or more biomarkers results in an increase in the level of the mRNA.
- the alteration in the level of one or more biomarkers results in an increase in the level of the protein.
- the sample is isolated from cells obtained by biopsy or any other method of extraction.
- the e determining the level comprises analyzing the sample for the level of DNA or RNA.
- the determining the level is carried out by (1) PCR amplification, SDA amplification, or any other method of nucleic acid amplification, (2) using a nucleic acid microarray, (3) gel electrophoresis, (4) transfer to a membrane and hybridization with a specific probe, and (5) diagnostic imaging.
- the determining the level comprises analyzing the sample for the level of the protein.
- the analysis is carried out by (1) incubation with a specific antibody, (2) Western blot, (3) immunohistochemistry, (4) gel electrophoresis, (5) microarray, (6) ELISA, and (7) diagnostic imaging.
- the variation in the expression levels of the gene or genes is used to predict the progression of the colorectal cancer or of a premalignant condition thereof, for predicting the risk of recurrence, and/or determining the type of therapy.
- the level of gene expression is determined by using probes.
- the probes are antibodies. In one embodiment, the antibodies are monoclonal. In one embodiment, the expression levels are determined by immunohistochemical staining of the biological sample.
- the expression profile is determined by quantifying a level of expression of one or more specific cellular protein.
- the specific cellular proteins are either involved in a biological pathway, belong to a group of proteins with identical or similar biological function, are expressed in a stage of cell cycle, expressed in a cell type, expressed in a tissue type, expressed in an organ type, or expressed in a developmental stage, proteins whose expression and/or activity is altered in a disease or disorder type or stage, or proteins whose expression, activity or a combination thereof is altered by a drug or other treatment.
- the specific cellular proteins comprise at least one transcription factor.
- the specific cellular proteins comprise at least one protein from the serine/threonine kinase family: MEK MKK3 PAK PAK6 CDK CDK8-LIKE MKK6 PAK4 CDK8 MKK4 PAK5 CDK9 MKK7 PAK3 NKIAMRE MEK5 PAKl KKIALRE MEK2 PAK2 KKIAMRE MEKl CaMK CASK STK9 MEKK TPL2 CAMKIIb CDK3 MEKK6 CAMKg CDK2 ASKl CAMK2A CDC2 MEKK2 CAMKIId CDK5 MEKK3 CAMKIId-Like CDK4 MEKK4 AMPKl-Like CDK6 MEKKl AMPKAl CCRK CKl CKIe PRKK-Like CDK7/CAK1 CKId SNFl-Like CDKlO CKla_Like STK29 PrrSLRE CK
- the specific cellular proteins comprise at least one protein from the tyrosine kinase family: JAK JAKl ABL ARG JAK2 ABL JAK3 TEC ITK TYK2 TEC SYK ZAP70 BTK SYK TXK SRC LYN BMX HCK FES FER BLK FES LCK ACK TNKl FYN ACKl FGR FAK FAK SRC PYK2 YESl MATK CSK FRK B.
- Receptor tyrosine kinases DDRl RET ERBB4 EPHA3 LMR2 DDR2 TIE ERBB2 EPHA5 LMRl ROS TEK ERBB3 EPHA4 AXL FLT3 EGFR EPHA7 MER FGFR4 EPHA8 SKY FGFR3 EPHBl MET FGFR2 EPHB2 RON FGFRl EPHB3 RYK VEGFRl EPHB4 TRKA VEGFR2 EPHB6 TRKB VEGFR3 EPHAl TRKC KIT EPHA2 MUSK CSFlR INSR CCK4 PDGFRA/B IGFlR ALK INSRR LTK ROR1/2.
- the specific cellular proteins comprise at least one transcription factor: ERK 1/2 EIk-I, Stat 1/3, Ets-1, ER, c-Myc, SRF, CREB SAPK/JNK c-Jun, ATF-2, EIk-I, p53, DPC4 p38 MAPK ATF-2, MEF2C, EIk-I, Myc/Max, Statl, CREB, CHOP ERK5/BMK MEF2C p90.sup.rsk c-Fos, SRF, CREB MSKl CREB JAKs STATs PKA CREB, SAF-I, GATA-4, SOX9, HNF-4, AR PKB/Akt forkhead, AFX GSK3.beta. API, beta-catenin, C/EBPalpha, CREB, HSF-I, Myc, NFAT, NF.kappa.B ALKs SMADs CaMK Ets-1,
- the specific cellular protein is selected from the group consisting of: Cyclin A, Cyclin B, Cyclin Dl, Cyclin D3, Cyclin E, CDKl, CDK2, CDK4, CDK6, E2F, CDC2, cdc25c, Cdc25A, Chk2, Chkl, pRb, p53, p21, p27, and Wee 1.
- the expression level is determined by determining the levels of a marker protein.
- the marker protein is selected from the group consisting of pl ⁇ 0 ⁇ 4* , HPV E6, HPV E7, HPV E2 HPV E4, HPV Ll, HPV L2, p27, p21, pl5, pl9, p53, pRb, and MDM2.
- the disease is a cell proliferative disorder, cancer or a precursor lesion.
- the cancer is cancer of the head and the neck, cancer of the respiratory tract, cancer of the gastrointestinal tract, cancer of the skin and its appendages, cancer of the central and peripheral nervous system, cancer of the urinary system, cancer of the reproductive system, anogenital cancer, cancer of the endocrine system, cancer of the soft tissues and bone, or cancer of the lymphopoietic and hematopoietic system.
- the reference gene expression profile comprises expression values of human mRNA for tyrosine phosphatase, X-linked mental retardation candidate gene, human interleukin-10 receptor mRNA, H-interferon inducible peptide, interferon-inducible 56 kD protein, insulin-like growth factor binding protein 5, winged helix transcription factor, interferon gamma, human mRNA zinc finger protein, apolipoprotein D precursor, a tumor suppressor protein or antigen, Homo sapiens Kueppel family zinc finger protein, major group rhinovirus receptor precursor, ICE like protease, caspase-10/b, and human transcription factor SIM2.
- the invention uses the gene expression profile of at least one tumor-suppressor gene such as the p53 gene, the Rb gene, etc.
- the tumor-suppressor gene is the Casp7 gene.
- the tumor-suppressor gene is the Dec gene.
- the tumor-suppressor gene is the p53 gene.
- the tumor- suppressor gene is one of several known tumor-suppressor genes, such as (RbI, WtI, NfI, Nf2, Ape, Tscl, Tsc2, Dpc4, Brcal, Brcal, Pten, Lkbl, Msh2, MM, CdM, VhI, Cdkn2a, Ptch, Menl, E2fl, Chek2, Cdknla, Smarcbl, Braf, Kit, Ret, Casp3, Egfr, Jun, Gstml, Gsttl, Mthfr, Gstpl, Cyplal, Xrccl, Ercc2, Nat2, Tnf IUb, IUO, and Ar).
- tumor-suppressor genes such as (RbI, WtI, NfI, Nf2, Ape, Tscl, Tsc2, Dpc4, Brcal, Brcal, Pten, Lkbl, Msh2, MM, C
- the practice of the present invention will employ, unless otherwise indicated, conventional techniques of molecular biology (including recombinant techniques), microbiology, cell biology, and biochemistry, which are within the skill of the art.
- conventional techniques of molecular biology including recombinant techniques
- microbiology including recombinant techniques
- cell biology including cell biology, and biochemistry
- Such techniques are explained fully in the literature, such as, "Molecular Cloning: A Laboratory Manual”, 2nd edition (Sambrook et al, 1989); “Oligonucleotide Synthesis” (M. J. Gait, ed., 1984); “Animal Cell Culture” (R. I. Freshney, ed., 1987); “Methods in Enzymology” (Academic Press, Inc.); “Handbook of Experimental Immunology", 4th edition (D. M. Weir & C. C.
- the detecting the expression of one or more marker that is specific for more than one proliferative disease comprises detecting the presence, absence, abundance and/or expression of physiological, genetic and/or cellular expression and/or cell count, preferably the detecting the expression comprises detecting the expression of protein, mRNA expression and/or the presence or absence of DNA methylation in one or more of the markers.
- the detecting the expression of protein comprises marker- specific antibodies, ELISA, cell sorting techniques, Western blot, or the detection of labeled protein
- the measuring the mRNA expression comprises detection of labeled mRNA or Northern blot.
- the determination of cancer comprises determining a chance of disease-free survival, and/or monitoring disease progression in the subject. In another embodiment, the determination of cancer comprises determining metastatic disease by identifying tissue markers in the sample that are foreign to the tissue from which the sample is taken from. In another embodiment, the proliferative disease is in the early pre-clinical stage exhibiting no clinical symptoms.
- methods of gene expression profiling can be divided into two large groups: methods based on hybridization analysis of polynucleotides, and methods based on sequencing of polynucleotides.
- the most commonly used methods known in the art for the quantification of mRNA expression in a sample include northern blotting and in situ hybridization (Parker & Barnes, Methods in Molecular Biology 106:247 283 (1999)); RNAse protection assays (Hod, Biotechniques 13:852 854 (1992)); and reverse transcription polymerase chain reaction (RT-PCR) (Weis et al, Trends in Genetics 8:263 264 (1992)).
- antibodies may be employed that can recognize specific duplexes, including DNA duplexes, RNA duplexes, and DNA-RNA hybrid duplexes or DNA-protein duplexes.
- Representative methods for sequencing-based gene expression analysis include Serial Analysis of Gene Expression (SAGE), and gene expression analysis by massively parallel signature sequencing (MPSS).
- RT-PCR which can be used to compare mRNA levels in different sample populations, in normal and tumor tissues, with or without drug treatment, to characterize patterns of gene expression, to discriminate between closely related mRNAs, and to analyze RNA structure.
- the first step is the isolation of mRNA from a target sample.
- the starting material is typically total RNA isolated from human tumors or tumor cell lines, and corresponding normal tissues or cell lines, respectively.
- RNA can be isolated from a variety of primary tumors, including breast, lung, colon, prostate, brain, liver, kidney, pancreas, spleen, thymus, testis, ovary, uterus, etc., tumor, or tumor cell lines, with pooled DNA from healthy donors.
- mRNA can be extracted, for example, from frozen or archived paraffin-embedded and fixed (e.g. formalin-fixed) tissue samples.
- RNA isolation can be performed using purification kit, buffer set and protease from commercial manufacturers, such as Qiagen, according to the manufacturer's instructions. For example, total RNA from cells in culture can be isolated using Qiagen RNeasy mini-columns.
- RNA isolation kits include MasterPure Complete DNA and RNA Purification Kit (EPICENTRE, Madison, Wis.), and Paraffin Block RNA Isolation Kit (Ambion, Inc.). Total RNA from tissue samples can be isolated using RNA Stat-60 (Tel-Test). RNA prepared from tumor can be isolated, for example, by cesium chloride density gradient centrifugation.
- RNA cannot serve as a template for PCR
- the first step in gene expression profiling by RT-PCR is the reverse transcription of the RNA template into cDNA, followed by its exponential amplification in a PCR reaction.
- the two most commonly used reverse transcriptases are avilo myeloblastosis virus reverse transcriptase (AMV-RT) and Moloney murine leukemia virus reverse transcriptase (MMLV-RT).
- AMV-RT avilo myeloblastosis virus reverse transcriptase
- MMLV-RT Moloney murine leukemia virus reverse transcriptase
- the reverse transcription step is typically primed using specific primers, random hexamers, or oligo-dT primers, depending on the circumstances and the goal of expression profiling.
- extracted RNA can be reverse-transcribed using a Gene Amp RNA PCR kit (Perkin Elmer, Calif., USA), following the manufacturer's instructions.
- the derived cDNA can then be used as a template
- the PCR step can use a variety of thermostable DNA-dependent DNA polymerases, it typically employs the Taq DNA polymerase, which has a 5'-3' nuclease activity but lacks a 3'-5' proofreading endonuclease activity.
- TaqMan PCR typically utilizes the 5'-nuclease activity of Taq or Tth polymerase to hydrolyze a hybridization probe bound to its target amplicon, but any enzyme with equivalent 5' nuclease activity can be used.
- Two oligonucleotide primers are used to generate an amplicon typical of a PCR reaction.
- a third oligonucleotide, or probe is designed to detect nucleotide sequence located between the two PCR primers.
- the probe is non-extendible by Taq DNA polymerase enzyme, and is labeled with a reporter fluorescent dye and a quencher fluorescent dye. Any laser- induced emission from the reporter dye is quenched by the quenching dye when the two dyes are located close together as they are on the probe.
- the Taq DNA polymerase enzyme cleaves the probe in a template-dependent manner.
- the resultant probe fragments disassociate in solution, and signal from the released reporter dye is free from the quenching effect of the second fluorophore.
- One molecule of reporter dye is liberated for each new molecule synthesized, and detection of the unquenched reporter dye provides the basis for quantitative interpretation of the data.
- TaqMan RT-PCR can be performed using commercially available equipment, such as, for example, ABI PRISM 7700 Sequence Detection System (Perkin- Elmer-Applied Biosystems, Foster City, Calif., USA), or Lightcycler (Roche Molecular Biochemicals, Mannheim, Germany).
- the 5' nuclease procedure is run on a real-time quantitative PCR device such as the ABI PRISM 7700 Sequence Detection System.
- the system consists of a thermocycler, laser, charge-coupled device (CCD), camera and computer.
- the system amplifies samples in a 96-well format on a thermocycler.
- laser-induced fluorescent signal is collected in real-time through fiber optics cables for all 96 wells, and detected at the CCD.
- the system includes software for running the instrument and for analyzing the data.
- 5'-Nuclease assay data are initially expressed as Ct, or the threshold cycle.
- Ct the threshold cycle
- fluorescence values are recorded during every cycle and represent the amount of product amplified to that point in the amplification reaction. The point when the fluorescent signal is first recorded as statistically significant is the threshold cycle (Ct).
- Ct the threshold cycle
- RT-PCR is usually performed using an internal standard. The ideal internal standard is expressed at a constant level among different tissues, and is unaffected by the experimental treatment. RNAs most frequently used to normalize patterns of gene expression are mRNAs for the housekeeping genes glyceraldehyde-3-phosphate- dehydrogenase (GAPDH) and .beta.-actin.
- GPDH glyceraldehyde-3-phosphate- dehydrogenase
- PCR which measures PCR product accumulation through a dual-labeled fluorigenic probe (i.e., TaqMan probe).
- Real time PCR is compatible both with quantitative competitive PCR, where internal competitor for each target sequence is used for normalization, and with quantitative comparative PCR using a normalization gene contained within the sample, or a housekeeping gene for RT- PCR.
- quantitative competitive PCR where internal competitor for each target sequence is used for normalization
- quantitative comparative PCR using a normalization gene contained within the sample, or a housekeeping gene for RT- PCR.
- PCR amplified inserts of cDNA clones are applied to a substrate in a dense array.
- Preferably at least 10,000 nucleotide sequences are applied to the substrate.
- the microarrayed genes, immobilized on the microchip at 10,000 elements each, are suitable for hybridization under stringent conditions.
- Fluorescently labeled cDNA probes may be generated through incorporation of fluorescent nucleotides by reverse transcription of RNA extracted from tissues of interest. Labeled cDNA probes applied to the chip hybridize with specificity to each spot of DNA on the array.
- the chip After stringent washing to remove non-specifically bound probes, the chip is scanned by confocal laser microscopy or by another detection method, such as a CCD camera. Quantitation of hybridization of each arrayed element allows for assessment of corresponding mRNA abundance. With dual color fluorescence, separately labeled cDNA probes generated from two sources of RNA are hybridized pairwise to the array. The relative abundance of the transcripts from the two sources corresponding to each specified gene is thus determined simultaneously. The miniaturized scale of the hybridization affords a convenient and rapid evaluation of the expression pattern for large numbers of genes.
- Microarray analysis can be performed by commercially available equipment, following manufacturer's protocols, such as by using the Affymetrix GenChip technology, or Incyte's microarray technology.
- the invention is applied to prostate cancer detection, it would be possible to detect cancer that was unsampled in a needle core biopsy by searching the entire length of the biopsy core for differential gene expression using immunohistchemistry. This is not the preferred method to detect cancer induced differential gene expression because of the time consuming nature of such a search.
- a search would need to be performed on all needle core biopsies taken from a patient. Most patients are sampled with ten or twelve needle core biopsies. The need to make lengthwise searches of ten or twelve biopsy cores per patient would be highly problematic due to the large human resources costs associated with this kind of search. Instead, we propose to search all of a patient's needle core biopsies in a single cytology specimen that is derived from the needle core biopsies.
- This cytology specimen is created when the needle core biopsies are fixed (such as with formalin) or possibly rinsed in an aqueous solution.
- the solution is an aqueous buffer about pH 6 to about pH 11, preferably an aqueous buffer about pH 7 to about pH 10, such as for example Phosphate Buffered Saline at pH 7.4.
- Fixation occurs in jars that are also used to transport specimens to pathology reference labs for further processing and evaluation.
- the needle core biopsies are placed in the fixative (and possibly other solutions as well) many cells detach from the biopsy core and become suspended in the fixative. These loose cells in the fixative are a sampling of the cells in the needle core biopsy.
- a cytology specimen would be created that consisted of a sampling of all (or some portion) of the needle core biopsies. Cells from this cytology specimen could be placed on a microscope slide and stained with an immunohistochemical (or an immunofluorescent or a molecular probe) reagent that could indicate the presence in a cell of a protein (or RNA) that was up-regulated or down-regulated due to the proximity of the cell in the prostate gland to a prostate tumor.
- an immunohistochemical or an immunofluorescent or a molecular probe
- Each field of view on such a microscope slide will contain many cells or clumps of cells each derived from a different part of one the various needle core biopsies from which the pooled cytology specimen was derived.
- the microscope slide by scanning one or a small number of fields on the microscope slide, one can quickly examine cells sampled from all portions of all needle core biopsies. If cells are identified that express one or more genes differentially in a pattern indicative of cancer , then the presence of prostate cancer is indicated even if no cancer is present in the tissue actually sampled by the needle core biopsies.
- AMACR alpha-Methylacyl coenzyme A racemase
- TMPRSSl Hepsin
- c-fos c-jun.
- Other genes are suggested by the work of Yu et al, (2004) and Chandran et al (2005).
- One embodiment of the current invention is the use of the cells, that detach from needle core prostate biopsy specimens when they are placed in fixative solution, as a cytology specimen to detect gene expression patterns in non-cancerous cells that are indicative of cancer that may not be directly observable in needle core biopsies from which this cytology specimen was derived.
- the sample according to the method of the present invention is any sample of cells or body fluids containing cellular components.
- samples may be for example gastrointestinal secretions, stool, bile, biopsies, cell- and tissue- samples.
- Biopsies as used in the context of the present invention may comprise e.g. resection samples of tumors, tissue samples prepared by endoscopic means or needle biopsies of organs.
- any sample potentially containing the nucleotides to be detected may be a sample according to the present invention.
- Such samples may comprise for example intact cells, lysed cells or any liquids containing proteins, peptides or nucleic acids. Even solids, to which cells, cell fragments or marker molecules may adhere, may be samples according to the present invention.
- preparation of a sample may comprise e.g. obtaining a sample of a tissue, a body fluid, of cells, of cell debris from a patient.
- preparation of the sample may also comprise several steps of further preparations of the sample, such as preparation of dissections, preparation of lysed cells, preparation of tissue arrays, isolation of polypeptides or nucleic acids, preparation of solid phase fixed peptides or nucleic acids or preparation of beads, membranes or slides to which the molecules to be determined are coupled covalently or non-covalently.
- a further embodiment of the current invention would be to examine expression patterns of more than one gene, including possibly both differentially expressed and non-differentially (constitutively) expressed genes, and combining the information from these various expression patterns in an analysis using a statistical algorithm to provide a better estimate of the probability of unseen cancer. This is a multivariate as opposed to a univariate analysis of the gene expression data.
- Another embodiment of the invention is the use of the cells as a cytology specimen to detect gene expression patterns in non-cancerous cells that are indicative of the cancer progression that may not be directly observable in needle core biopsies from which this cytology specimen was derived.
- the increased expression of the genes maybe down-regulated or up-regulated as indicative of cancer progression.
- Another embodiment of the invention is to examine gene expression patterns of one or more genes of metastatic cancer to detect the level of expression in anatomically normal or noncancerous cells in a cytology specimen as indicative of metastatic cancer or nonmetastatic cancer.
- Another embodiment of the invention would be to examine in morphologically benign cells the expression levels of genes known to be differentially expressed as a result of having been in the proximity of cancer.
- Examples of such examined differentially expressed genes may include, among others, one or more of the following genes: FGFR4, c-FOS, BTG2, IER2, c-Jun, JunD, JunB, CYR61, CyclinDl, EGRl, AMACR, Duffy Blood Group antigen and CD 163.
- one or more genes could be examined that are known not to be differentially expressed or only minimally differentially expressed. Examples of such non- differentially expressed genes that may be examined include, among other possible genes: HPRTl, ALASl, Tubulin-a, GAPDH and the androgen receptor. In this embodiment, the expression levels of examined genes may be evaluated individually.
- the expression levels of some or all of the examined genes may be compared to each other generating an expression level ratio.
- These expression level ratios and/or individual gene expression levels would comprise the input variables that would be analyzed by a statistical algorithm the output of which would be the probability of unseen or unsampled cancer or prognostic and/or predictive information about a patient's cancer (whether directly observed or not).
- This statistical algorithm may be derived from any of a variety of statistical methods such as but not limited to logistical regression, artificial neural networks, principle component analysis, support vector machines or other methods.
- the method is also applicable to the detection of bladder cancer, its progression level and whether it is metastatic or nonmetastatic cancer. Every year, tens of thousands of patients are diagnosed with bladder cancer. In addition, there are hundreds of thousands of patients who have been previously diagnosed with and treated for bladder cancer. These previously diagnoses and treated patients are monitored for recurrence of their disease.
- cytology specimens are loose cells derived from the lining of the bladder or other parts of the urinary system and are collected in either urine or bladder lavages.
- Pathologists examine bladder cytology specimens for the presence of cancer cells. Large numbers of noncancerous cells may also be present in the cytology specimen. Identifying bladder cancer with a cytology specimen can be problematic due to imperfect sensitivity and specificity.
- the means to increase the performance of bladder cytology is to examine the noncancerous cells in the cytology specimen for cancer specific gene expression patterns that arose in these cells due to their proximity to cancer cells when they were embedded in the lining of the urinary system.
- this analysis of the expression patterns in bladder cytologies can be performed using immunohistochemical, immunofluorescent or a molecular probe reagent(s) that can be analyzed by either a univariate or multivariate method using a statistical algorithm.
- the method can also apply to the detection, progression level and differentiation of metastatic from nonmetastatic breast cancer.
- Fine needle aspirate (FNA) biopsy specimens of the breast can be used to detect breast cancer. This is a cytology specimen that is examined by a pathologist in an attempt to detect cancer cells. Similarly to the applications described for prostate and bladder cancer, this method suffers from imperfect sensitivity and specificity.
- FNA FNA
- This analysis of the expression patterns in FNAs can be performed using immunohistochemical or immunoperoxidase, immunofluorescent or a molecular probe reagent(s) that can be analyzed by either a univariate or multivariate method using a statistical algorithm.
- breast cancer can also be diagnosed with needle core biopsies. It is envisioned that a cytology specimen could be created from a breast needle core biopsy in a manner identical to that for a prostate needle core biopsy described previously. Normal or non-cancerous cells from such cytology specimens could also be examined for indications of cancer just as described for the prostate specimens.
- the methods of the present invention are not limited to prostate, bladder or breast cancer.
- the current invention can be used to improve the detection of cancer in any directly obtained cytology specimen or cytology specimens resulting from cell dispersion into fixative solutions or other solutions.
- the key to all applications of the current invention is to examine the normal and/or noncancerous cells in such cytology specimens to identify altered patterns of gene expression that arose in these cells as a result of their proximity to cancer in the organ from which the cytology specimen was derived.
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CHENG Q ET AL: "Identification of molecular markers for the early detection of human squamous cell carcinoma of the uterine cervix", BRITISH JOURNAL OF CANCER, NATURE PUBLISHING GROUP, LONDON, GB, vol. 86, no. 2, 21 January 2002 (2002-01-21), pages 274-281, XP002447748, ISSN: 0007-0920, DOI: 10.1038/SJ.BJC.6600038 * |
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